AMBER Archive (2008)

Subject: Re: AMBER: 3fe-4s cluster parameter file generation

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Mon Sep 15 2008 - 12:21:44 CDT

before making topology just check the molecule structure in leap, it will be
wrongly bonded , if it display a bond between the fe-fe, then you have
remove and make topology

On Mon, Sep 15, 2008 at 5:36 PM, <moitrayee_at_mbu.iisc.ernet.in> wrote:

> I have modified the prepc file as :-
>
> 0 0 2
>
> This is a remark line
> molecule.reS
> F3S XYZ 0
> CHANGE OMIT DU BEG
> 0.0000
> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 S1 S S 0.402592 -1.514288 -1.117435 -0.15436
> 5 S2 S S -1.882611 0.670231 -0.727350 -0.17413
> 6 S3 S B 0.078709 -0.205500 1.731896 -0.31438
> 7 S4 S S 1.046182 1.057400 -1.309825 -0.13664
> 8 FE1 FE B -1.129336 -1.094156 0.156620 0.63632
> 9 FE2 FE B 1.553155 -0.302094 0.294594 0.59276
> 10 FE3 FE B -0.205279 1.391423 0.424303 0.55042
>
>
> LOOP
>
> IMPROPER
>
> DONE
> STOP
> The pdb of the ligand is as follows:
>
>
> ATOM 22415 FE1 F3S 2476 22.031 131.687 125.051 1.00 3.44
> FE
> ATOM 22416 FE3 F3S 2476 19.837 133.121 124.065 1.00 8.66
> FE
> ATOM 22417 FE4 F3S 2476 22.106 132.579 122.776 1.00 2.99
> FE
> ATOM 22418 S1 F3S 2476 19.888 131.269 124.910 1.00 16.32
> S
> ATOM 22419 S2 F3S 2476 21.822 130.489 123.262 1.00 18.57
> S
> ATOM 22420 S3 F3S 2476 21.887 133.677 124.533 1.00 26.75
> S
> ATOM 22421 S4 F3S 2476 20.081 132.614 122.029 1.00 28.82
> S
> But even then i am getting the same error asking for an fe-fe bond length
> parameter,etc while trying to create the topology files using Leap. Please
> suggest me what should i do ?
>
> Sincere Regards,
> Moitrayee
>
>
> > On Mon, Sep 15, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
> >
> >> I did not use antechamber but manually did it using the co-ordinate and
> charge
> >> information from the Gaussian single point calculation. The prepc file
> is
> >> given
> >> below:
> >>
> >> 0 0 2
> >>
> >> This is a remark line
> >> molecule.res
> >> F3S XYZ 0
> >> CHANGE OMIT DU BEG
> >> 0.0000
> >> 1 DUMM DU M 999.000 999.0 -999.0
> .00000
> >> 2 DUMM DU M 999.000 -999.0 999.0
> .00000
> >> 3 DUMM DU M -999.000 999.0 999.0
> .00000
> >> 4 S1 S M 0.402592 -1.514288 -1.117435
> -0.15436
> >> 5 S2 S M -1.882611 0.670231 -0.727350
> -0.17413
> >> 6 S3 S M 0.078709 -0.205500 1.731896
> -0.31438
> >> 7 S4 S M 1.046182 1.057400 -1.309825
> -0.13664
> >> 8 FE1 FE M -1.129336 -1.094156 0.156620
> 0.63632
> >> 9 FE2 FE M 1.553155 -0.302094 0.294594
> 0.59276
> >> 10 FE3 FE M -0.205279 1.391423 0.424303
> 0.55042
> >
> > The above is wrong: you have every atom as a "mainchain" atom, so the
> > covalent structure implied above is S1-S2-S3-S4-Fe1-Fe2-Fe3, which is,
> > of course, not what you want.
> >
> > ...dac
> >
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-- 
S.Sundar Raman
CSIR-SRF
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai, India- 600 020
&
DAAD Research Scholar
Hause No. 5, Room No. 106
Ulmenweg 55, Mannheim, Germany - 68167

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